Poison Ivy could also be a main antagonist. She could use her plant - based powers to create chaos in both Central City and Gotham. She might try to take over Gotham first, using her plants to strangle the city, and then spread to Central City. The Flash and Batman would have to find a way to stop her without harming the innocent plants she controls.
The Riddler could be a great main antagonist. He could create puzzles and traps that are based on both the Flash's speed and Gotham's dark secrets. For example, he might set up a trap where the Flash has to run through a maze of moving walls in Gotham while also solving riddles that are related to Batman's past.
A new meta - human villain created specifically for the crossover could be interesting. This villain could have the power to control shadows and use them to move quickly, mimicking the Flash's speed in a way. In Gotham, he could use the city's many dark corners and alleys to his advantage. He could also be a master of disguise, fooling both the Flash and Batman. His motives could be to take over both Gotham and Central City and create a new world order where meta - humans rule over normal humans.
The Reverse - Flash would be a great antagonist. His time - traveling abilities and his vendetta against the Flash family could make for a really intense story, especially if he teams up with other villains from the Kid Flash's universe in a crossover.
Darth Vader could be a great main antagonist. His power in the Force and his imposing presence would be a huge threat to The Flash. He could try to capture The Flash to study his speed abilities for the Empire.
Perhaps a rogue demigod who has made a deal with a speed - based meta - human villain from the Flash's world. Together, they plan to take over both the magical realm and Central City. The demigod could use his powers in combination with the meta - human's technology to create some really tough challenges for Percy and the Flash.
The Riddler could be a great main antagonist. He could use his intellect to create puzzles and traps that not only challenge Batman's detective skills but also the Flash's speed. For example, he could set up a series of time - locked puzzles where the Flash has to use his speed in a very specific way at specific times to unlock them, while Batman has to figure out the overall pattern of the puzzles.
It could be a time - traveling villain. Since the story involves watching the future, a villain who can manipulate time would be a great fit. This villain could be trying to change the future for his own evil purposes, and The Flash has to stop him to preserve the good future.
If it's a crossover with Alice in Wonderland, the Queen of Hearts could be the main antagonist. The Queen might see Tinkerbell as an intruder and try to behead her. Tinkerbell would have to use her wits and magic to survive in the crazy world ruled by the Queen of Hearts.
In a Gotham Flash crossover fanfiction, perhaps there's a device that disrupts the speed force and it's located in Gotham. The Flash has to go there to fix it. He meets the various characters in Gotham like the Joker, who tries to use the Flash's powers for his own chaos. Meanwhile, Flash has to work with the likes of Gordon and Robin to stop the Joker and repair the device. The different moral compasses of the Gothamites and the Flash could lead to some interesting character interactions.
A powerful demon from another dimension could be the main antagonist. This demon could be attracted to the power that Sinbad wields in the Magi world and wants to steal it for himself. He could start causing chaos in both the world Sinbad is from and the world he's been transported to in the crossover.
A new character could be introduced as the main antagonist. For example, a being from another dimension who has been observing both Sonic's and Megaman's worlds. This being realizes that by combining the chaos energy from Sonic's world and the advanced robotics technology from Megaman's world, it can create a new, all - powerful empire. So it starts to manipulate events in both worlds to bring about this combination, while Sonic and Megaman have to stop it.